Postgraduate clinical training for dentists in Japan became mandatory in April 2006. Mandatory postgraduate clinical training for physicians has been criticized as having accelerated the imbalance in distribution of physicians. This suggests the danger that the same phenomenon might occur in distribution of dentists. It is also necessary to investigate the geographic distribution of dental trainees and practicing dentists in Japan. In this study, the number of dental trainees enrolled in each clinical training program and number that had actually received clinical training at each facility were compared by prefecture. The results suggest that disparities in the number of dental trainees among prefectures are being compensated for by movement across prefectural borders under the clinical training facilities-group system. Postgraduate dental trainees, however, showed a significantly greater imbalance in geographic distribution than practicing dentists. Continuation of the postgraduate clinical training for dentists under the existing system may accelerate this imbalance in distribution of dentists. To prevent this, practical measures should be taken in accordance with the coming review of the system, based on research regarding changes in geographic distribution of dental trainees.